Contacts of the helix formed by residues 164 - 178 (chain D) in PDB entry 2D11
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with THR 164 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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162D LYS* 4.5 7.4 - - - +
163D LEU* 1.3 77.1 - - - +
165D LYS* 1.3 65.5 + - - +
166D GLU* 3.4 22.5 + - - +
167D GLN* 2.9 50.9 + - - +
168D TRP* 3.1 13.2 + - - -
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Residues in contact with LYS 165 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147D LEU 5.0 0.2 + - - -
148D ALA* 3.2 35.7 + - - +
150D ASP 5.7 3.6 + - - -
158D LEU* 6.4 0.4 - - - -
163D LEU 4.1 0.2 + - - -
164D THR* 1.3 72.7 - - - +
166D GLU* 1.3 66.2 + - - +
168D TRP* 3.3 12.8 + - - +
169D GLU* 2.8 55.1 + - - +
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Residues in contact with GLU 166 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145D GLY* 6.5 0.2 - - - -
164D THR* 3.4 25.5 + - - +
165D LYS* 1.3 80.3 + - - +
167D GLN* 1.3 63.7 + - + +
169D GLU* 3.4 17.3 + - - +
170D GLU* 3.0 26.9 + - - +
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Residues in contact with GLN 167 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162D LYS* 4.9 0.8 + - - +
163D LEU* 3.5 30.5 - - + +
164D THR* 2.9 52.2 + - - +
166D GLU* 1.3 77.3 - - + +
168D TRP* 1.3 64.6 + - - +
170D GLU* 3.2 16.9 + - - +
171D ARG* 3.0 27.4 + - + +
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Residues in contact with TRP 168 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119D PRO* 4.8 8.5 - - + -
123D VAL* 3.4 33.0 - - + -
153D LEU* 3.9 20.2 - - + -
157D VAL* 3.8 28.0 - - + -
158D LEU* 3.7 31.3 + - + +
161D HIS* 4.0 26.4 - + + +
163D LEU* 3.6 45.4 + - + +
164D THR 3.1 21.7 + - - -
165D LYS* 3.3 11.4 + - - +
167D GLN* 1.3 75.0 - - - +
169D GLU* 1.3 64.0 + - + +
171D ARG* 3.3 20.1 + - + +
172D ILE* 3.1 29.3 + - + +
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Residues in contact with GLU 169 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145D GLY* 4.1 15.5 - - - +
147D LEU* 3.8 27.0 - - + +
148D ALA* 3.9 22.6 + - - +
152D LEU* 5.1 5.2 - - + -
165D LYS* 2.8 53.2 + - + +
166D GLU* 3.5 18.0 + - - +
167D GLN 3.2 0.2 - - - -
168D TRP* 1.3 75.2 - - + +
170D GLU* 1.3 57.9 + - - +
172D ILE* 3.2 9.0 + - + +
173D GLN* 2.8 34.7 + - - +
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Residues in contact with GLU 170 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166D GLU 3.0 13.3 + - - +
167D GLN* 3.2 21.5 + - - +
169D GLU* 1.3 77.0 - - - +
171D ARG* 1.3 56.8 + - + +
173D GLN* 3.5 15.9 + - - +
174D ASN* 3.0 50.2 + - - +
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Residues in contact with ARG 171 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120D GLU* 2.5 40.2 + - - -
123D VAL* 3.8 20.5 - - + +
163D LEU* 4.1 21.0 - - + +
167D GLN* 3.0 18.0 + - + +
168D TRP* 3.5 31.4 - - + +
169D GLU 3.2 0.4 - - - -
170D GLU* 1.3 74.7 - - + +
172D ILE* 1.3 63.6 + - - +
174D ASN* 3.6 14.7 + - - +
175D TRP* 3.6 12.2 + - - -
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Residues in contact with ILE 172 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123D VAL* 3.9 22.4 - - + +
126D ALA* 3.9 14.1 - - + -
127D SER* 3.7 29.3 - - - +
130D VAL* 3.8 20.4 - - + -
147D LEU* 4.4 5.2 - - + -
152D LEU* 3.7 22.9 - - + -
153D LEU* 3.7 24.9 - - + -
168D TRP 3.1 18.1 + - - +
169D GLU* 3.8 6.1 - - + +
171D ARG* 1.3 72.6 - - - +
173D GLN* 1.3 62.0 + - - +
175D TRP* 3.1 6.8 + - - +
176D HIS* 2.9 24.5 + - - +
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Residues in contact with GLN 173 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137D TYR* 3.7 15.7 + - + -
142D HIS 4.9 1.5 - - - +
144D PRO* 4.4 19.4 - - - +
145D GLY 5.0 1.4 - - - +
146D TYR* 3.3 45.6 - - + +
147D LEU* 4.1 1.7 - - + +
169D GLU* 2.8 16.9 + - - +
170D GLU* 3.6 18.3 - - - +
172D ILE* 1.3 76.7 - - - +
174D ASN* 1.3 61.7 + - - +
176D HIS* 3.2 3.4 + - - +
177D GLU* 2.9 49.0 + - - +
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Residues in contact with ASN 174 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170D GLU* 3.0 35.2 + - - +
171D ARG* 3.8 11.8 - - - +
172D ILE 3.2 0.4 - - - -
173D GLN* 1.3 82.2 + - - +
175D TRP* 1.3 62.1 + - + +
177D GLU* 3.8 29.2 + - - +
178D GLU* 3.4 24.3 - - - +
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Residues in contact with TRP 175 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120D GLU* 5.1 9.3 + - - +
123D VAL* 3.9 26.3 - - + +
124D LEU* 3.7 41.7 - - + +
127D SER* 3.4 21.3 - - - -
128D TYR* 5.6 0.7 - - - -
171D ARG* 3.6 7.2 + - - -
172D ILE* 3.1 5.4 + - - +
174D ASN* 1.3 77.0 - - + +
176D HIS* 1.3 67.3 + - - +
178D GLU* 2.9 40.3 + - + +
179D HIS* 3.5 26.3 + + - -
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Residues in contact with HIS 176 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127D SER* 3.8 2.8 - - - +
130D VAL* 3.5 32.4 + - + +
131D GLN* 3.2 30.5 + - + +
134D TYR* 4.4 3.4 - - + -
135D GLY 3.1 22.4 + - - -
137D TYR* 3.7 31.9 + + - +
142D HIS* 4.2 8.7 - + - -
146D TYR* 3.0 31.3 + + - +
172D ILE 2.9 13.6 + - - +
173D GLN* 3.2 9.2 + - - +
175D TRP* 1.3 75.1 - - - +
177D GLU* 1.3 61.8 + - - +
179D HIS* 3.0 24.6 + - - +
180D ARG 4.2 0.3 + - - -
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Residues in contact with GLU 177 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137D TYR* 3.6 45.3 + - + -
173D GLN* 2.9 41.5 + - - +
174D ASN* 3.8 21.5 + - - +
175D TRP 3.2 0.2 + - - -
176D HIS* 1.3 75.7 - - - +
178D GLU* 1.3 62.6 + - + +
179D HIS 3.3 1.1 + - - -
180D ARG* 3.9 24.4 + - - +
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Residues in contact with GLU 178 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174D ASN* 3.4 21.1 - - - +
175D TRP* 2.9 35.8 + - + +
177D GLU* 1.3 79.4 - - + +
179D HIS* 1.3 64.2 + - + +
180D ARG* 3.4 4.4 + - - +
182D MET* 5.9 0.5 - - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il